LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors
  special bonds CPU = 0.00199628 secs
  read_data CPU = 0.0169649 secs

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles
  find clusters CPU = 0.000807762 secs

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 103823 64000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50    4782.1702    4728.7435    328.28767    53.426722    1812.2203    685.37824    683.70917   -3277.1645    797.34329    1305983.2   -1306631.2    16874.358    48631.318    448.52419    116.25477 
     100    2906.0879    3699.8031    256.85465    -793.7152    978.15364    778.36908    862.30899   -3270.1722    468.44888    1306096.8   -1306707.6    15631.384    48631.318    382.26408    35.748403 
     150    2089.0918    3593.0499    249.44342   -1503.9581    751.32283    803.47802     668.4757   -3277.5983    128.17444    1306138.5   -1306716.3     15193.04    48631.318    384.75632    10.892446 
     200    1547.3302     3248.639    225.53309   -1701.3089    699.65977    814.31164    692.83227   -3276.3957   -66.671816    1306160.9   -1306725.9    13787.676    48631.318    351.28242    3.8458668 
     250    1177.9323     3095.949    214.93276   -1918.0167    688.87262    842.44531    615.89218   -3278.4465   -210.06178    1306154.3     -1306731    8808.5835    48631.318     335.8115    1.8330994 
     300    895.90313    2870.3451    199.27046    -1974.442    734.95873    858.58147    624.00862   -3278.6022   -342.01951    1306163.6     -1306735    3388.4841    48631.318    311.56815    1.2987715 
     350    669.25785    2764.9587    191.95413   -2095.7009    662.44028    860.79714    602.69567    -3278.776   -376.37081    1306172.3   -1306738.8    8494.9184    48631.318    300.19414    1.1358594 
     400    531.21609    2722.6775    189.01881   -2191.4614    684.34049    868.77818    576.86096   -3280.1649   -459.66591      1306160   -1306741.6    6726.3087    48631.318    295.59622    1.1315427 
     450    427.05425    2611.7588     181.3184   -2184.7046     719.2042    891.88178     591.2282    -3279.339   -534.65069    1306172.2   -1306745.2    2398.5394    48631.318    283.56126    1.0726045 
     500    310.44891    2556.0967    177.45412   -2245.6477    720.86526    841.50195     586.3417   -3279.3029   -539.81715    1306169.5   -1306744.8     3028.595    48631.318    277.52314    1.0406334 
     550    207.83114    2531.3051    175.73299   -2323.4739    674.71188     855.2132    555.53227   -3280.0378   -553.93222    1306171.9   -1306746.9    4609.4408    48631.318    274.80629    1.0748601 
     600     88.81557    2459.9059    170.77619   -2371.0903     692.4485    834.47484    550.85905   -3280.9086   -595.31802    1306171.4     -1306744    2107.9995    48631.318    267.06312    1.0301965 
     650    75.616307    2416.9747    167.79573   -2341.3584    703.57186    869.98959    564.81201   -3280.7522    -619.8016      1306168   -1306747.2    1236.4829    48631.318     262.3542    1.0968447 
     700    49.832719    2415.7344    167.70963   -2365.9017    683.61663    882.67915    555.23571   -3280.7778   -615.06862    1306159.9   -1306751.4    2985.7048    48631.318    262.23095    1.0762424 
     750    41.513638     2427.218    168.50687   -2385.7044    698.87619     863.2938    564.58197   -3280.0156   -637.29964    1306160.1   -1306755.3     1653.117    48631.318    263.49803    1.0451977 
     800    109.53032    2481.9041    172.30339   -2372.3738    697.22709    897.36555    561.28745   -3280.6784   -651.29564      1306155   -1306751.3    1219.8761    48631.318    269.43698    1.0647792 
     850    98.142203    2502.3132    173.72026    -2404.171     696.5382    878.83293    566.44302   -3280.2837   -663.94587    1306155.6   -1306757.4    1122.7487    48631.318    271.67716     1.030267 
     900    62.992675    2409.7324    167.29295   -2346.7397    722.00541    896.64662    560.66083   -3279.4915   -644.05458    1306153.6   -1306756.1     1604.295    48631.318    261.58656    1.0609836 
     950    5.6677468    2403.5067    166.86073    -2397.839    725.07222    891.00249    556.81977   -3279.7848   -672.66389      1306141   -1306759.2    1019.1694    48631.318    260.91187    1.0562387 
    1000    38.526968      2444.97    169.73928   -2406.4431    704.72993    920.68493    534.59035   -3281.2673   -667.78091    1306141.1   -1306758.5    486.79846    48631.318    265.39928     1.098473 
    1050    21.698026    2388.6306    165.82798   -2366.9326    712.15539    934.39244    546.92027   -3281.1469    -654.7449    1306137.4   -1306761.9    1556.1256    48631.318    259.28203    1.0760765 
    1100   -26.971225    2433.8428    168.96678    -2460.814    710.11081    881.19212    524.51547   -3281.7925   -667.53202    1306137.1   -1306764.4    1203.8971    48631.318    264.20441    1.0706085 
    1150   -49.171269    2375.9688    164.94895     -2425.14    729.78127    918.79575    518.21967   -3281.6542    -675.7239    1306130.4     -1306765    229.44016    48631.318    257.89845     1.086519 
    1200   -53.421342    2422.0091    168.14524   -2475.4304    710.67274     884.2589    523.32524   -3282.2275   -674.49333    1306130.9   -1306767.9   -131.09655    48631.318    262.91124    1.0804821 
    1250   -58.534776    2394.4031    166.22873   -2452.9378    680.27486    909.58096    532.81959   -3281.5551   -653.13731      1306127   -1306767.9    546.96357    48631.318    259.92916    1.0424914 
    1300   -24.151217    2431.9902    168.83817   -2456.1414    681.27127    919.39245    536.41899   -3281.3717   -661.90875    1306121.6   -1306771.5    1455.7512    48631.318    264.00712    1.0630558 
    1350   -38.973062    2438.6194     169.2984   -2477.5925    707.96118    912.62518    519.44533   -3281.6739   -687.67183    1306126.1   -1306774.4   -1470.4442    48631.318    264.70225    1.1091537 
    1400    11.896539    2384.5407    165.54404   -2372.6442    719.03374    950.93261     550.5639   -3280.4581    -663.4921      1306122   -1306771.3    465.12854    48631.318    258.83564    1.0785364 
    1450   -13.118691    2436.6246    169.15991   -2449.7433    661.04397    933.07103    561.29537   -3280.6997   -672.68495    1306123.9   -1306775.7   -108.46564    48631.318    264.50636    1.0718787 
    1500   -38.151755    2417.4849    167.83116   -2455.6367    688.81484    892.35701    565.29013   -3279.6716    -662.1817    1306116.9   -1306777.2    517.89634    48631.318    262.44549    1.0338083 
    1550   -71.663334    2405.7016    167.01311   -2477.3649    681.78925    876.31247      559.003    -3280.451   -649.16641    1306112.8   -1306777.7    925.49349    48631.318      261.148    1.0609731 
    1600   -13.900431     2419.481    167.96973   -2433.3814    718.46559    909.67964    559.06779   -3280.8163    -667.6092      1306108   -1306780.2     13.95808    48631.318    262.63632     1.080229 
    1650   -16.403222     2431.075    168.77464   -2447.4783    710.99509    907.65662    551.60307   -3279.8852   -661.52624    1306104.5   -1306780.8    726.89923    48631.318    263.91553    1.0489963 
    1700   -18.555086    2438.2062    169.26971   -2456.7613    665.90475    943.02217    542.86579   -3280.9017   -657.99229      1306108   -1306777.7    801.41078    48631.318    264.67663    1.0750708 
    1750   -6.9249446    2443.9707     169.6699   -2450.8956    733.23573    890.06857    560.83229    -3280.362   -670.93883    1306098.3   -1306782.1    47.037748    48631.318    265.30892    1.0661143 
    1800   -21.686222    2434.3375    169.00113   -2456.0237    729.35297     899.9733    561.59516   -3280.4727   -680.98901    1306096.5     -1306782    495.63617    48631.318    264.25723    1.0723683 
    1850   -72.916947    2408.8254    167.22998   -2481.7423    683.24984    904.13282    549.97726   -3279.6699   -652.63212    1306099.2     -1306786   -120.61674    48631.318    261.48504    1.0659808 
    1900     -55.4099     2415.455    167.69023   -2470.8649     700.4473    904.72264     565.5266   -3280.4533   -673.23082    1306099.6   -1306787.4    202.15936    48631.318    262.20353    1.0709756 
    1950   -79.877997    2409.2307    167.25812   -2489.1087     695.9536     894.4541     564.7034   -3279.3581   -680.33472    1306100.8   -1306785.3    213.72828    48631.318    261.52921    1.0658433 
    2000   -102.20457    2399.4263    166.57746   -2501.6309    689.67819    894.58596    565.53233   -3280.7595   -680.39032    1306096.4   -1306786.6    1113.7499    48631.318    260.46311    1.0647045 
Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms

Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 48.825     | 48.825     | 48.825     |   0.0 | 71.36
Bond    | 2.8852     | 2.8852     | 2.8852     |   0.0 |  4.22
Kspace  | 13.795     | 13.795     | 13.795     |   0.0 | 20.16
Neigh   | 1.0731     | 1.0731     | 1.0731     |   0.0 |  1.57
Comm    | 0.27067    | 0.27067    | 0.27067    |   0.0 |  0.40
Output  | 0.0031168  | 0.0031168  | 0.0031168  |   0.0 |  0.00
Modify  | 1.5207     | 1.5207     | 1.5207     |   0.0 |  2.22
Other   |            | 0.04541    |            |       |  0.07

Nlocal:    5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    13157 ave 13157 max 13157 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1338215
Ave neighs/atom = 243.312
Ave special neighs/atom = 15.6364
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:01:08
